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swc2vtk

travisci Coverage Status python-2.7,3.3,3.4-blue license paraview NEURON

SWC to VTK converter for visualizing neurons and neural circuit simulations in ParaView.
This software helps making easy and beautiful visualization of large scale multi-compartmental neuron simulation with highly parallelized environments.

Dependency

  • tqdm
  • numpy
  • PyVTK

Install

  • $ pip install swc2vtk

Usage

Basic way to generate VTK file from one SWC file

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.write_vtk('simple.vtk')

generate a VTK file from multiple SWC files

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.add_swc('simple1.swc')
vtkgen.add_swc('simple2.swc')
vtkgen.write_vtk('combined.vtk')

generate a VTK file from SWC file with simulation data

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.add_datafile('result.dat')
vtkgen.write_vtk('simple.vtk')
  • data example
    each rows correspondence to SWC compartments
-65.0
-65.0
-65.0
-65.0

generate VTK files from SWC file with sequential simulation data

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')

vtkgen.add_datafile('result1.dat')
vtkgen.write_vtk('simple1.vtk')

vtkgen.clear_datafile()
vtkgen.add_datafile('result2.dat')
vtkgen.write_vtk('simple2.vtk')

vtkgen.clear_datafile()
vtkgen.add_datafile('result3.dat')
vtkgen.write_vtk('simple3.vtk')

generate VTK file for volume rendering

import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.write_volume_vtk('volume.vtk')

Settings

Visualization Quality

  • Draw Mode change SWC compartment drawing method. Largeer number is better.
    • 0: simple cylinder
    • 1: one cylinder with variable top surface
    • 2: one cylinder with three cell mode
    • 3: one cylinder with a hemisphere
import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.set_draw_mode(4)
vtkgen.write_vtk('simple.vtk')
  • Division Number
import swc2vtk
vtkgen = swc2vtk.VtkGenerator()
vtkgen.add_swc('simple.swc')
vtkgen.set_division_number(20)
vtkgen.write_vtk('simple.vtk')

adjust compartment diameter

  • normalize_diam

Output Examples

Single Neuron Morphology

single

Coloring Multiple SWC Files

Coloring

Single Neuron Simulation

Neural Circuit Simulation

Volume Rendering

References